4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
28 package org.forester.surfacing;
30 import java.util.SortedMap;
31 import java.util.SortedSet;
33 import org.forester.protein.BinaryDomainCombination;
34 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
35 import org.forester.species.Species;
36 import org.forester.util.DescriptiveStatistics;
38 public interface GenomeWideCombinableDomains {
40 public boolean contains( String key_id );
42 public CombinableDomains get( String key_id );
44 public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds();
47 * This should return all domains ids present in the genome.
49 * @return a sorted set of domains ids
51 public SortedSet<String> getAllDomainIds();
53 public DomainCombinationType getDomainCombinationType();
56 * This should return a statistic for per domain
57 * promiscuity in a genome.
59 * @return descriptive statistics for per domain promiscuity in a genome
61 public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics();
65 public Species getSpecies();
68 * This should return all binary domain combinations present in the genome.
70 * @return a sorted set of binary domain combinations
72 public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations();
74 public StringBuilder toStringBuilder( GenomeWideCombinableDomainsSortOrder order );
76 SortedSet<String> getMostPromiscuosDomain();
78 public static enum GenomeWideCombinableDomainsSortOrder {
79 ALPHABETICAL_KEY_ID, COMBINATIONS_COUNT, KEY_DOMAIN_COUNT, KEY_DOMAIN_PROTEINS_COUNT